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The Plant Genome : Just Published


Accepted, edited articles are published here after author proofing to provide rapid publication and better access to the newest research. Articles are compiled into issues at dl.sciencesocieties.org/publications/tpg, which includes the complete archive.

Citation | Articles posted here are considered published and may be cited by the doi.

Joseph, B., J.A. Schlueter, J.Du, M.A. Graham, J. Ma, and R.C. Shoemaker. 2009. Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution. Plant Genome doi:10.3835/plantgenome2009.01.0001

Current issue: Plant Genome 10(2)


    • Neele Wendler, Martin Mascher, Axel Himmelbach, Federica Bini, Jochen Kumlehn and Nils Stein
      A High-Density, Sequence-Enriched Genetic Map of Hordeum bulbosum and Its Collinearity to H. vulgare

      Hordeum bulbosum L., a wild grass and close relative of cultivated barley (Hordeum vulgare L.), gained importance in plant breeding as inducer of haploid plants in crosses with barley and also as a genetic resource for introgression of disease resistance/tolerance genes into cultivated barley. Genetic mapping of genes introgressed from H. bulbosum is a prerequisite for their efficient utilization in barley breeding, but often hindered due to repressed recombination. The mechanism underlying the reduced frequency or lack of meiotic recombination between H. (continued)

      Core Ideas:
      • Genotyping-by-sequencing was used to create high-density genetic maps of the out-crossing species Hordeum bulbosum
      • Collinearity was compared between the created H. bulbosum genetic maps and genetic maps of barley
      • A de novo H. bulbosum assembly was generated using a doubled haploid H. bulbosum plant and gene models were predicted on the assembly
      • H. bulbosum de novo contigs were integrated into the genetic maps to construct an anchored sequence reference of H. bulbosum

      Published: October 12, 2017

    • Jason D. Fiedler, Evan Salsman, Yuan Liu, Monika Michalak de Jiménez, Justin B. Hegstad, Bingcan Chen, Frank A. Manthey, Shiaoman Chao, Steven Xu, Elias M. Elias and Xuehui Li
      Genome-Wide Association and Prediction of Grain and Semolina Quality Traits in Durum Wheat Breeding Populations

      Grain yield and semolina quality traits are essential selection criteria in durum wheat breeding. However, high phenotypic screening costs limit selection to relatively few breeding lines in late generations. This selection paradigm confers relatively low selection efficiency due to the advancement of undesirable lines into expensive yield trials for grain yield and quality trait testing. Marker-aided selection can enhance selection efficiency, especially for traits that are difficult or costly to phenotype. (continued)

      Core Ideas:
      • Genome-wide association and prediction for grain and semolina quality traits were performed using elite durum wheat breeding populations.
      • Several QTL for test weight, semolina color, and gluten strength were detected.
      • Forward prediction accuracies of 0.27–0.66 were obtained for the quality traits using genome-wide markers.
      • Implementation of genomics-assisted breeding could enhance selection efficiency for grain and semolina quality traits in durum wheat breeding program.

      Published: October 12, 2017

    • Xiaofei Zhang, Steven R. Larson, Liangliang Gao, Soon Li Teh, Lee R. DeHaan, Max Fraser, Ahmad Sallam, Traci Kantarski, Katherine Frels, Jesse Poland, Donald Wyse and James A. Anderson
      Uncovering the Genetic Architecture of Seed Weight and Size in Intermediate Wheatgrass through Linkage and Association Mapping

      Intermediate wheatgrass [IWG; Thinopyrum intermedium (Host) Barkworth & D.R. Dewey subsp. intermedium] is being developed as a new perennial grain crop that has a large allohexaploid genome similar to that of wheat (Triticum aestivum L.). Breeding for increased seed weight is one of the primary goals for improving grain yield of IWG. (continued)

      Core Ideas:
      • Twenty-three shared QTL were identified using linkage and association mapping
      • Overlapped QTL explained the high genetic correlation among seed weight and size
      • QTL responded positively to either phenotypic selection or genomic selection
      • Combining association mapping and genomic selection would increase genetic gain

      Published: October 5, 2017

    • Theresa A. Hill, Jareerat Chunthawodtiporn, Hamid Ashrafi, Kevin Stoffel, Allyson Weir and Allen Van Deynze
      Regions Underlying Population Structure and the Genomics of Organ Size Determination in Capsicum annuum

      Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers (Capsicum annuum L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large-fruited, nonpungent types have reduced diversity and comprise a highly structured group. (continued)

      Core Ideas:
      • The genomes of hot peppers versus sweet peppers were compared.
      • Genomic regions that were polymorphic in hot peppers but not polymorphic in sweet peppers were detected.
      • These regions overlap with quantitative trait loci (QTLs) and genes determining pepper fruit size and pungency.
      • There are hotspots for fruit size QTLs in the genome.

      Published: October 5, 2017

    • Xiaofei Wang, Qianli Dong, Xiaochong Li, Anzhi Yuliang, Yanan Yu, Ning Li, Bao Liu and Lei Gong
      Cytonuclear Variation of Rubisco in Synthesized Rice Hybrids and Allotetraploids

      The allopolyploid speciation process faces the genomic challenge of stoichiometric disruption caused by merging biparental nuclear genomes with only one (usually maternal) of the two sets of progenitor cytoplasmic genomes. The photosynthetic protein 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is composed of nuclear-encoded small subunits (SSUs) and plastome-encoded large subunits (LSUs), making it an ideal enzyme to explore the evolution process of cytonuclear accommodation. We investigated the variation of SSUs and their encoding rbcS genes in synthetic nascent rice (Oryza sativa L.) allotetraploid lineages, formed from the parental subspecies japonica and indica of Asian rice. The evolution of rbcS genes in rice subspecies involves both mutation and concerted homogenization. (continued)

      Core Ideas:
      • This study addressed an underexplored dimension about cytonuclear coordination or coevolution in allopolyploid speciation, caused by duplicated nuclear genomes in the context of only one set of organellar genomes.
      • This study characterized the evolutionary features of rbcS genes in diploid rice subspecies and investigated the cytonuclear coevolution of Rubisco genes (biparentally inherited nuclear rbcS and unimaternal plastid rbcL genes encoding small subunits and large subunits, respectively) in synthesized rice hybrids (9N and N9) and allotetraploids (99NN and NN99).
      • Within reciprocal rice hybrids and allopolyploids, there was no consistent pattern of biased expression of rbcS alleles or homoeologs, nor was there biased gene conversion favoring the maternal gene copies.
      • It was concluded that cytonuclear coordination in the present rice case either is not selectively favored because of high parental sequence similarity, or that there has been insufficient time for subtle selective effects to become observable.

      Published: September 28, 2017

    • Marnin D. Wolfe, Dunia Pino Del Carpio, Olumide Alabi, Lydia C. Ezenwaka, Ugochukwu N. Ikeogu, Ismail S. Kayondo, Roberto Lozano, Uche G. Okeke, Alfred A. Ozimati, Esuma Williams, Chiedozie Egesi, Robert S. Kawuki, Peter Kulakow, Ismail Y. Rabbi and Jean-Luc Jannink
      Prospects for Genomic Selection in Cassava Breeding

      Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. (continued)

      Core Ideas:
      • Accuracy is generally similar across breeding populations.
      • Data sharing across programs improves predictions in some circumstances.
      • Accuracy across generations is sufficient for rapid-cycling genomic selection (GS) on several traits.
      • Phenotyping small numbers of progeny can have a large impact on prediction accuracy.
      • Prospects for GS in cassava are good and improving.

      Published: September 28, 2017

    • Münevver Doğramaci, James V. Anderson, Wun S. Chao, David P. Horvath, Alvaro G. Hernandez, Mark A. Mikel and Michael E. Foley
      Foliar Glyphosate Treatment Alters Transcript and Hormone Profiles in Crown Buds of Leafy Spurge and Induces Dwarfed and Bushy Phenotypes throughout its Perennial Lifecycle

      Leafy spurge (Euphorbia esula L.) is an invasive weed of North America and its perennial nature attributed to underground adventitious buds (UABs) that undergo seasonal cycles of para-, endo-, and ecodormancy. Recommended rates of glyphosate (∼1 kg ha–1) destroy aboveground shoots but plants still regenerate vegetatively; therefore, it is considered glyphosate-tolerant. However, foliar application of glyphosate at higher rates (2.2–6.7 kg ha–1) causes sublethal effects that induce UABs to produce stunted, bushy phenotypes. We investigated the effects of glyphosate treatment (±2.24 kg ha–1) on vegetative growth, phytohormone, and transcript profiles in UABs under controlled environments during one simulated seasonal cycle. (continued)

      Core Ideas:
      • Continuous increases in glyphosate-resistant weeds mandates a better understanding of glyphosate’s effects on plant physiology.
      • Higher rates (2.24–6.74 kg ha–1) of foliar-applied glyphosate can cause a sublethal effect in the underground portion of leafy spurge and induce altered vegetative growth patterns from underground buds in the following shoot generations.
      • We investigated the effects of glyphosate treatment (±2.24 kg ha–1) on vegetative growth and metabolite and transcript profiles in underground buds of leafy spurge under controlled environments during its perennial lifecycle.

      Published: September 14, 2017

    • Sandeep R. Marla, Sunitha Shiva, Ruth Welti, Sanzhen Liu, John J. Burke and Geoffrey P. Morris
      Comparative Transcriptome and Lipidome Analyses Reveal Molecular Chilling Responses in Chilling-Tolerant Sorghums

      Chilling temperatures (0 to 15°C) are a major constraint for temperate cultivation of tropical-origin crops, including the cereal crop sorghum (Sorghum bicolor [L.] Moench). Northern Chinese sorghums have adapted to early-season chilling, but molecular mechanisms of chilling tolerance are unknown. We used RNA sequencing of seedlings to compare the chilling-responsive transcriptomes of a chilling-tolerant Chinese accession with a chilling-sensitive US reference line, and mass spectrometry to compare chilling-responsive lipidomes of four chilling-tolerant Chinese accessions with two US reference lines. Comparative transcriptomics revealed chilling-induced up-regulation of cold-response regulator C-repeat binding factor (CBF) transcription factor and genes involved in reactive oxygen detoxification, jasmonic acid (JA) biosynthesis, and lipid remodeling phospholipase Dα1 (PLDα1) gene in the chilling-tolerant Chinese line. (continued)

      Core Ideas:
      • Functional genomics approaches were used to understand sorghum chilling responses
      • CBF signaling and phytohormone jasmonic acid likely contribute to sorghum chilling tolerance
      • Lipid remodeling may be a chilling adaptation mechanism in Chinese sorghums
      • These molecular chilling responses could be targets for molecular breeding

      Published: September 14, 2017

    • Kebede T. Muleta, Peter Bulli, Zhiwu Zhang, Xianming Chen and Michael Pumphrey
      Unlocking Diversity in Germplasm Collections via Genomic Selection: A Case Study Based on Quantitative Adult Plant Resistance to Stripe Rust in Spring Wheat

      Harnessing diversity from germplasm collections is more feasible today because of the development of lower-cost and higher-throughput genotyping methods. However, the cost of phenotyping is still generally high, so efficient methods of sampling and exploiting useful diversity are needed. Genomic selection (GS) has the potential to enhance the use of desirable genetic variation in germplasm collections through predicting the genomic estimated breeding values (GEBVs) for all traits that have been measured. Here, we evaluated the effects of various scenarios of population genetic properties and marker density on the accuracy of GEBVs in the context of applying GS for wheat (Triticum aestivum L.) germplasm use. (continued)

      Core Ideas:
      • Larger germplasm collections may be efficiently sampled via lower-density genotyping methods.
      • The selection population needs to be well represented in the training set.
      • Good prospects for applying genomic selection to efficiently unlock the potential of plant genetic resources exist.

      Published: August 10, 2017

    • Birgit Samans, Boulos Chalhoub and Rod J. Snowdon
      Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus

      Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of Brassica napus L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. (continued)

      Core Ideas:
      • Homeologous chromosome exchanges drive postpolyploidization genetic diversification in Brassica napus.
      • Homeologous exchanges cause rapid genome size reduction after allopolyploidization.
      • Segmental deletions contain genes associated with adaptive processes and chromosome stability.
      • Breakpoints of genomic rearrangements contain motifs associated with meiotic recombination.
      • Genes involved in chromosome mismatch repair are subject to selection after polyploidization.

      Published: August 10, 2017

    • Sarah R. Braun, Jeffrey B. Endelman, Kathleen G. Haynes and Shelley H. Jansky
      Quantitative Trait Loci for Resistance to Common Scab and Cold-Induced Sweetening in Diploid Potato

      The development of germplasm with resistance to common scab and cold-induced sweetening is a high priority for the potato (Solanum tuberosum L.) industry. A mapping population was developed from mating two individuals of a diploid family generated by crossing the susceptible cultivated potato clone US-W4 to the highly resistant wild relative (Solanum chacoense Bitter) clone ‘524–8’. Progeny were evaluated in replicated field trials. Tubers were scored for percentage of surface area with scab lesions, scab lesion type, cold-induced sweetening, average tuber weight, and dry matter. (continued)

      Core Ideas:
      • Resistance to common scab and cold-induced sweetening is important to the potato industry.
      • A quantitative trait locus (QTL) for resistance to common scab was identified on chromosome 11.
      • Two QTLs for resistance to cold-induced sweetening were identified on chromosomes 4 and 6.
      • Additional QTLs were detected for vine maturity and tuber weight.
      • This is the first step in the development of molecular markers for use by breeders.

      Published: August 10, 2017

    • Samar O. Rabah, Chaehee Lee, Nahid H. Hajrah, Rania M. Makki, Hesham F. Alharby, Alawiah M. Alhebshi, Jamal S.M. Sabir, Robert K. Jansen and Tracey A. Ruhlman
      Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew

      In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative rpl22 in cinnamon (Cinnamomum verum J. (continued)

      Core Ideas:
      • DNA sequence data provides valuable information for biotechnology and evolutionary studies.
      • Plastid genomes (plastomes) of 10 nonmodel crop species were sequenced.
      • Inversions, gene divergence and loss, and IR boundary variation were identified.
      • Transfer of mitochondrial DNA to the plastome was found in Anacardium (cashew).

      Published: August 3, 2017

    • Ismail Y. Rabbi, Lovina I. Udoh, Marnin Wolfe, Elizabeth Y. Parkes, Melaku A. Gedil, Alfred Dixon, Punna Ramu, Jean-Luc Jannink and Peter Kulakow
      Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

      Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. (continued)

      Core Ideas:
      • Cassava, a starchy root crop, is a major source of dietary calories in the tropics.
      • Most varieties consumed are poor in micronutrients, including pro-vitamin A.
      • Dry matter and carotenoid content are governed by few major loci on chromosome 1.
      • Genetic linkage, rather than pleiotropy, is the most likely cause of their negative correlation.

      Published: August 3, 2017

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